[2023-03-18 01:08:39,052] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:08:39,052] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:08:39,053] [INFO] DQC Reference Directory: /var/lib/cwl/stg80420314-085b-4df9-9f89-57feb1da7d78/dqc_reference
[2023-03-18 01:08:40,180] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:08:40,181] [INFO] Task started: Prodigal
[2023-03-18 01:08:40,181] [INFO] Running command: cat /var/lib/cwl/stgd8c3ede8-a958-44f6-be37-a053630c7e31/OceanDNA-b24045.fa | prodigal -d OceanDNA-b24045/cds.fna -a OceanDNA-b24045/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:08:58,444] [INFO] Task succeeded: Prodigal
[2023-03-18 01:08:58,444] [INFO] Task started: HMMsearch
[2023-03-18 01:08:58,444] [INFO] Running command: hmmsearch --tblout OceanDNA-b24045/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80420314-085b-4df9-9f89-57feb1da7d78/dqc_reference/reference_markers.hmm OceanDNA-b24045/protein.faa > /dev/null
[2023-03-18 01:08:58,644] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:08:58,644] [INFO] Found 6/6 markers.
[2023-03-18 01:08:58,674] [INFO] Query marker FASTA was written to OceanDNA-b24045/markers.fasta
[2023-03-18 01:08:58,674] [INFO] Task started: Blastn
[2023-03-18 01:08:58,674] [INFO] Running command: blastn -query OceanDNA-b24045/markers.fasta -db /var/lib/cwl/stg80420314-085b-4df9-9f89-57feb1da7d78/dqc_reference/reference_markers.fasta -out OceanDNA-b24045/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:08:59,319] [INFO] Task succeeded: Blastn
[2023-03-18 01:08:59,321] [INFO] Selected 39 target genomes.
[2023-03-18 01:08:59,321] [INFO] Target genome list was writen to OceanDNA-b24045/target_genomes.txt
[2023-03-18 01:08:59,352] [INFO] Task started: fastANI
[2023-03-18 01:08:59,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8c3ede8-a958-44f6-be37-a053630c7e31/OceanDNA-b24045.fa --refList OceanDNA-b24045/target_genomes.txt --output OceanDNA-b24045/fastani_result.tsv --threads 1
[2023-03-18 01:09:27,365] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:27,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80420314-085b-4df9-9f89-57feb1da7d78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:09:27,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80420314-085b-4df9-9f89-57feb1da7d78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:09:27,376] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:09:27,376] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:09:27,376] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.1741	60	947	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.0152	74	947	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.983	68	947	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.8765	90	947	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.8587	84	947	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.7373	70	947	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	75.7029	54	947	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_014197775.1	1086	1086	type	True	75.7	54	947	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_004341375.1	1086	1086	type	True	75.7	54	947	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	75.652	53	947	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.5983	57	947	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	75.552	56	947	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.5156	82	947	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.365	87	947	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.365	87	947	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	75.3273	52	947	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.296	67	947	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.1751	89	947	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:09:27,376] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24045/tc_result.tsv
[2023-03-18 01:09:27,377] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:09:27,377] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:09:27,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80420314-085b-4df9-9f89-57feb1da7d78/dqc_reference/checkm_data
[2023-03-18 01:09:27,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:09:27,382] [INFO] Task started: CheckM
[2023-03-18 01:09:27,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24045/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24045/checkm_input OceanDNA-b24045/checkm_result
[2023-03-18 01:10:14,562] [INFO] Task succeeded: CheckM
[2023-03-18 01:10:14,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:10:15,034] [INFO] ===== Completeness check finished =====
[2023-03-18 01:10:15,034] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:10:15,034] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24045/markers.fasta)
[2023-03-18 01:10:15,035] [INFO] Task started: Blastn
[2023-03-18 01:10:15,036] [INFO] Running command: blastn -query OceanDNA-b24045/markers.fasta -db /var/lib/cwl/stg80420314-085b-4df9-9f89-57feb1da7d78/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24045/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:10:16,166] [INFO] Task succeeded: Blastn
[2023-03-18 01:10:16,167] [INFO] Selected 38 target genomes.
[2023-03-18 01:10:16,167] [INFO] Target genome list was writen to OceanDNA-b24045/target_genomes_gtdb.txt
[2023-03-18 01:10:16,197] [INFO] Task started: fastANI
[2023-03-18 01:10:16,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8c3ede8-a958-44f6-be37-a053630c7e31/OceanDNA-b24045.fa --refList OceanDNA-b24045/target_genomes_gtdb.txt --output OceanDNA-b24045/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:10:42,255] [INFO] Task succeeded: fastANI
[2023-03-18 01:10:42,267] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:10:42,267] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_018660305.1	s__JABJKO01 sp018660305	76.4911	138	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__JABJKO01	95.0	99.60	99.60	0.81	0.81	2	-
GCA_905181725.1	s__UBA830 sp905181725	76.2581	84	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284725.1	s__Phaeospirillum kuznetsovii	76.1741	60	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002239065.1	s__MPNO01 sp002239065	76.1124	145	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__MPNO01;g__MPNO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674495.1	s__GCA-2687515 sp018674495	76.0775	76	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2687515	95.0	99.77	99.72	0.95	0.94	13	-
GCF_902729425.1	s__Phaeospirillum sp902729425	76.0582	73	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003285.1	s__JABDJY01 sp013003285	76.0573	57	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	75.983	68	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006218045.1	s__Magnetospirillum sp006218045	75.8741	62	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.95	99.95	0.98	0.98	2	-
GCA_902729415.1	s__Phaeospirillum magnetica_A	75.8206	56	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	75.8118	59	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479125.1	s__UBA830 sp905479125	75.7239	86	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	-
GCF_001703635.1	s__Hoeflea olei	75.652	53	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184795.1	s__Phaeospirillum sp900184795	75.6465	72	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009985.1	s__Phaeospirillum magneticum	75.6444	73	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576635.1	s__Skermanella stibiiresistens	75.5156	82	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377535.1	s__WHTV01 sp009377535	75.4819	71	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858635.1	s__Telmatospirillum sp903858635	75.4455	67	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	99.88	99.86	0.92	0.90	3	-
GCF_900177295.1	s__Tistlia consotensis	75.3764	86	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_903918315.1	s__CAIXEA01 sp903918315	75.2979	50	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	99.91	99.85	0.96	0.93	5	-
GCF_003258835.1	s__Rhodobium orientis	75.2693	65	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2023-03-18 01:10:42,268] [INFO] GTDB search result was written to OceanDNA-b24045/result_gtdb.tsv
[2023-03-18 01:10:42,268] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:10:42,270] [INFO] DFAST_QC result json was written to OceanDNA-b24045/dqc_result.json
[2023-03-18 01:10:42,270] [INFO] DFAST_QC completed!
[2023-03-18 01:10:42,270] [INFO] Total running time: 0h2m3s